{"action":"created","issue":{"url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/2","repository_url":"https://api.github.com/repos/bio-phys/PyDHAMed","labels_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/2/comments","events_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/2/events","html_url":"https://github.com/bio-phys/PyDHAMed/issues/2","id":272022398,"number":2,"title":"last_g_zero=True sometimes gives an error ","user":{"login":"lukas-stelzl","id":20243278,"avatar_url":"https://avatars1.githubusercontent.com/u/20243278?v=4","gravatar_id":"","url":"https://api.github.com/users/lukas-stelzl","html_url":"https://github.com/lukas-stelzl","followers_url":"https://api.github.com/users/lukas-stelzl/followers","following_url":"https://api.github.com/users/lukas-stelzl/following{/other_user}","gists_url":"https://api.github.com/users/lukas-stelzl/gists{/gist_id}","starred_url":"https://api.github.com/users/lukas-stelzl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukas-stelzl/subscriptions","organizations_url":"https://api.github.com/users/lukas-stelzl/orgs","repos_url":"https://api.github.com/users/lukas-stelzl/repos","events_url":"https://api.github.com/users/lukas-stelzl/events{/privacy}","received_events_url":"https://api.github.com/users/lukas-stelzl/received_events","type":"User","site_admin":false},"labels":[{"id":741268947,"url":"https://api.github.com/repos/bio-phys/PyDHAMed/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":{"login":"lukas-stelzl","id":20243278,"avatar_url":"https://avatars1.githubusercontent.com/u/20243278?v=4","gravatar_id":"","url":"https://api.github.com/users/lukas-stelzl","html_url":"https://github.com/lukas-stelzl","followers_url":"https://api.github.com/users/lukas-stelzl/followers","following_url":"https://api.github.com/users/lukas-stelzl/following{/other_user}","gists_url":"https://api.github.com/users/lukas-stelzl/gists{/gist_id}","starred_url":"https://api.github.com/users/lukas-stelzl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukas-stelzl/subscriptions","organizations_url":"https://api.github.com/users/lukas-stelzl/orgs","repos_url":"https://api.github.com/users/lukas-stelzl/repos","events_url":"https://api.github.com/users/lukas-stelzl/events{/privacy}","received_events_url":"https://api.github.com/users/lukas-stelzl/received_events","type":"User","site_admin":false},"assignees":[{"login":"lukas-stelzl","id":20243278,"avatar_url":"https://avatars1.githubusercontent.com/u/20243278?v=4","gravatar_id":"","url":"https://api.github.com/users/lukas-stelzl","html_url":"https://github.com/lukas-stelzl","followers_url":"https://api.github.com/users/lukas-stelzl/followers","following_url":"https://api.github.com/users/lukas-stelzl/following{/other_user}","gists_url":"https://api.github.com/users/lukas-stelzl/gists{/gist_id}","starred_url":"https://api.github.com/users/lukas-stelzl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukas-stelzl/subscriptions","organizations_url":"https://api.github.com/users/lukas-stelzl/orgs","repos_url":"https://api.github.com/users/lukas-stelzl/repos","events_url":"https://api.github.com/users/lukas-stelzl/events{/privacy}","received_events_url":"https://api.github.com/users/lukas-stelzl/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2017-11-07T23:28:21Z","updated_at":"2017-11-16T20:19:45Z","closed_at":null,"author_association":"MEMBER","body":"ZeroDivisionError                         Traceback (most recent call last)\r\n<ipython-input-36-882a6db4a90e> in <module>()\r\n----> 1 og = run_dhamed(c_l, -np.log(v_ar), g_init=og, numerical_gradients=False, last_g_zero=True)\r\n\r\n/Users/lukas/Projects/DHAMed/public-dhamed/PyDHAMed/pydhamed/optimize_dhamed.pyc in grad_dhamed_likelihood_ref_0(g_prime, g, ip, jp, ti, tj, vi, vj, nk, nijp)\r\n     88     grad = np.zeros(g.shape[0] )\r\n     89     grad[:-1]  += nk[:-1]\r\n---> 90     grad = loop_grad_dhamed_likelihood_0(grad,g, ip, jp, ti, tj, vi, vj, nijp)\r\n     91     return grad[:-1]\r\n     92 \r\n\r\nZeroDivisionError: division by zero"},"comment":{"url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/comments/345050283","html_url":"https://github.com/bio-phys/PyDHAMed/issues/2#issuecomment-345050283","issue_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/2","id":345050283,"user":{"login":"lukas-stelzl","id":20243278,"avatar_url":"https://avatars1.githubusercontent.com/u/20243278?v=4","gravatar_id":"","url":"https://api.github.com/users/lukas-stelzl","html_url":"https://github.com/lukas-stelzl","followers_url":"https://api.github.com/users/lukas-stelzl/followers","following_url":"https://api.github.com/users/lukas-stelzl/following{/other_user}","gists_url":"https://api.github.com/users/lukas-stelzl/gists{/gist_id}","starred_url":"https://api.github.com/users/lukas-stelzl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukas-stelzl/subscriptions","organizations_url":"https://api.github.com/users/lukas-stelzl/orgs","repos_url":"https://api.github.com/users/lukas-stelzl/repos","events_url":"https://api.github.com/users/lukas-stelzl/events{/privacy}","received_events_url":"https://api.github.com/users/lukas-stelzl/received_events","type":"User","site_admin":false},"created_at":"2017-11-16T20:19:45Z","updated_at":"2017-11-16T20:19:45Z","author_association":"MEMBER","body":"Hi Laura,\r\nThanks so much for your comment, that's very helpful! \r\n\r\n\"last_g_zero\" sets the the log-weight of the last state to zero. This we can do, as we are only interested in the relative free energies. Doing so restricts the space for the solution and should help. One thing, that I should probably change is that the output array has to be multiplied by minus to be a PMF. \r\n\r\nI'm travelling until Tuesday, but I'm very keen to get to the bottom of this once I'm back! "}}
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